Local background correction

Prerequisites
Before starting this lesson, you should be familiar with:

Median filter

Projections

Learning Objectives
After completing this lesson, learners should be able to:

Understand how to use image filters for creating a local background image

Use the generated local background image to compute a foreground image

Motivation

Very often, biological images contain locally varying background intensities. This hampers both segmentation and intensity quantification. However, often it is possible to generate a background image that can be subtracted in order to yield a foreground image with zero background. It is very important to know about this, because removing spatially varying background is a prevalent task in bioimage analysis.

Concept map

graph TD ii(Input image) ii --> bgi[Background image] bgi --> s[Subtract] ii --> s s --> fgi[Foreground image]

Figure

Local background correction using a median filter. Left - Raw data. Middle - Median filtered image (background). Right - Difference image (foreground).

Activities

Background subtraction using a median filter

Open image xy_8bit__some_spots_with_uneven_bg
Compute a background image using a median filter
Create a foreground image by subtracting the background image from the input image
(Optional) Segment the spots in the foreground image.

Show activity for:

ImageJ GUI

Open image xy_8bit__some_spots_with_uneven_bg

[ Image › Rename… ]

“input”

Create background image

[ Image > Duplicate…]

[ Process > Filters > Median… ]

radius = 15

[ Image › Rename… ]

“background”

Create foreground image

[ Process › Image Calculator… ]

Image 1 = input

Subtract

Image 2 = background

create

32-bit

[ Image › Rename… ]

“foreground”

ImageJ Macro

/**
 * Fiji script for local background subtraction 
 */

// Parameters (please modify)
//
medianFilterRadius = 15;

// Code (rather not modify)
//
run("Close All");

// Open data
open("https://github.com/NEUBIAS/training-resources/raw/master/image_data/xy_8bit__some_spots_with_uneven_bg.tif");
rename("input");

// Create background image
run("Duplicate...", "title=background");
run("Median...", "radius="+medianFilterRadius);
rename("background");

// Create foreground image
imageCalculator("Subtract create 32-bit", "input","background");
rename("foreground");

run("Tile");

// Create line profiles for a more quantitative visualisation of the process
makeLine(99,200,81,121,82,87,91,64,230,26);
selectWindow("foreground");
run("Plot Profile");

// Also create the same line profiler on the input image
selectWindow("input");
run("Restore Selection");
run("Plot Profile");

skimage napari

# %% [markdown]
# ### Background subtraction using a median filter
# From teaching module [Local background correction](https://neubias.github.io/training-resources/local_background_correction/index.html#bgmedian)

# %%
import numpy as np

# Instantiate the napari viewer
import napari
viewer = napari.Viewer()

# Read the intensity image
from OpenIJTIFF import open_ij_tiff
image, axes, scales, units = open_ij_tiff('https://github.com/NEUBIAS/training-resources/raw/master/image_data/xy_8bit__some_spots_with_uneven_bg.tif')

# View the intensity image
viewer.add_image(image, name='original image')

# Inspect image data type and values
print('image type:', image.dtype,'\n',
      'image shape:', image.shape,'\n',
      'intensity min:',   np.min(image),'\n',
      'intensity max:',   np.max(image),'\n'
      )

# %% [markdown]
# Compute background image with the median filter from skimage
# %%
from skimage import filters
from skimage.morphology import disk

# Median filtering with radius 15
# Structuring element - aka footprint is disk
background = filters.median(image, disk(15))
viewer.add_image(background, name='background')

# %% [markdown]
# Compute a foreground image by subtracting the background image from the raw image

# %%
# Convert/cast to signed int16 and subtract. 
# A subtraction can cause negative values and we would like to keep these values
foreground = image.astype('int16') - background.astype('int16')
viewer.add_image(foreground, name='foreground')

# %% [markdown]
# **Napari GUI** \
# Inspect the intensity image values in order to identify a threshold
# that segments cells \
# Hover with mouse, line profile

# %%
# Threshold the image
binary_image_cells = foreground > 8
# Overlay the binary image
viewer.add_image(binary_image_cells, name='segmented image')


# %% [markdown]
# ### Learning opportunity: Effect of radius on local background subtraction
# Modify radius of median filter and compute a new foreground image\
# For example try a radius of 3 and of 50\
# Discuss the different results

Background subtraction using a maximum intensity projection

Open image xyt_8bit_polyp
Create a maximum intensity projection of this image.
Because the polyp is moving around and is darker than the background this will create a background image.
Create a foreground image by subtracting the maximum intensity projection from the original image.

Show activity for:

ImageJ GUI

Open image xyt_8bit_polyp

Make a maximum intensity projection to create a background image ([Image › Stacks › Z Project…])

Use the image calculator function [ Process › Image Calculator…] to subtract the maximum intensity projection from the original:

Image1: xyt_8bit_polyp

Operation: Subtract

Image2: MAX_xyt_8bit_polyp

‘create new window’

‘32-bit float result’

Say ‘yes’ to the ‘Process entire stack’ message.

ImageJ Macro

// Open image
open("https://github.com/NEUBIAS/training-resources/raw/master/image_data/xyt_8bit_polyp.tif");
// Create maximum intensity projection
run("Z Project...", "projection=[Max Intensity]");
// Subtract maximum intensity projection from original image
imageCalculator("Subtract create 32-bit stack", "xyt_8bit_polyp.tif","MAX_xyt_8bit_polyp.tif");

ImageJ Jython

# Use a maximum intensity projection for background subtraction

# import packages
from ij import IJ
from ij.plugin import ZProjector, ImageCalculator

# open image
imp = IJ.openImage("https://github.com/NEUBIAS/training-resources/raw/master/image_data/xyt_8bit_polyp.tif")

# create maximum intensity projection
maxproj = ZProjector().run(imp, "max all")

# subtract maximum intensity projection from original image
background_subtracted = ImageCalculator().run(imp, maxproj, "Subtract create 32-bit stack")

# show all images
imp.show()
maxproj.show()
background_subtracted.show()
IJ.run("Tile")

skimage napari

# %% [markdown]
# ### Background subtraction using a maximum intensity projection
# Activity is part of the teaching module [Local background correction](https://neubias.github.io/training-resources/local_background_correction/index.html#bgmaxima)

# %%
import numpy as np
# Read the intensity image
from OpenIJTIFF import open_ij_tiff
image, axes, scales, units = open_ij_tiff('https://github.com/NEUBIAS/training-resources/raw/master/image_data/xyt_8bit_polyp.tif')

# Inspect image data type and values
print('image type:', image.dtype,'\n',
      'image shape:', image.shape,'\n',
      'intensity min:',   np.min(image),'\n',
      'intensity max:',   np.max(image),'\n'
      'axis order:', axes
      )

# %%
# Instantiate the napari viewer
import napari
viewer = napari.Viewer()
viewer.add_image(image, name='original image')

# %%
# Remember the axis order 0=t, 1=x, 2=y
# Maximum projection along t-axis
max_t_image = np.max(image, axis = 0)
viewer.add_image(max_t_image, name = 'background')

# %%
# Cast to signed int16 to include also negative values
foreground = image.astype('int16') - max_t_image.astype('int16')
viewer.add_image(foreground, name = 'foreground')

Assessment

True or false?

Mean filter is better than the median filter to generate a background image.
On the generated background image the objects of interest should not be visible.
When creating a background image by means of filtering: The size of the filter’s structuring element should be much smaller than the size of the objects.

Solution

False (mean filter is really quite poor in terms of removing foreground information)

True (because this is the background image, so it should not contain any foreground information)

False (it should be much (maybe ~3 times) larger in order to remove the objects from the image)

Explanations

There exist multiple methods on how to compute a background image. Which methods and parameters work best depends on the specific input image and the size of the object of interest.

Common methods are:

Median filtering
Morphological opening. Subtraction of the opened image from the original image is also called Top-Hat filtering.
Rolling ball, this alogorithm is implemented for instance in ImageJ Background Subtraction or skimage.restoration.rolling_ball

Some of the methods may be sensistive to noise. Therefore, it can be convenient to smooth the image, e.g. with a mean or gaussian filtering, prior computing the background image.

Follow-up material

Recommended follow-up modules:

Morphological filtering

Learn more: